Hi,

I'm trying to make a PCA plot of an RUVs-corrected SeqExpressionSet object and would like to add labels. I'm using the function 'plotPCA' from the EDAseq package with the following code:

plotPCA(set1, labels=F, pch=as.numeric(batch))

Although there is a labels argument in the plotPCA function, I would like to know how to retain the pch symbols and also add labels underneath my points.

Thanks in advance for your help!